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My 2003 E39 M5 needs a new battery. I'm trying to find
a place that is close to home (downtown TO) that will sell
a replacement or OEM, for a "reasonable" amount. I looked
on http://www.autopartsway.ca, but they don't even list a
battery.

Can someone please recommend a good place to find a
battery locally ? I know I can get one in Niagara Falls for $165

Iirc, all batteries are put in designation categories.
Go to a local NApa or something and get them to look up a battery, they will tell you what the disgnation is which fits. There is nothing special about an M5 battery, you just need one that has the + and - on the right side (if it even matters) and it fits in the tray and provide the output which is necessary for the V8.

From my experience, my Range rover, my e34 M5 and current M5 use pretty much the same battery.

I bought a battery for my e34 from Eurostyle (it was used but only 1.5 years old for cheap) and when I needed to get one for my RR I got one from Napa for like 140 bucks or something where the dealer wanted 3-400$.

Actually, the battery for a E39 M5 is quite different than anything I've
seen before. First, it huge and designed to fit in a tight space in the trunk.
The battery is vented and has two handles on it. What I found was that
there were only two or three replacement batteries that would even fit
in the battery compartment properly. Other batteries may work, but they
don't fit without adding risers and spacers to position and hold the battery
in place.

BMW Toronto wanted $405 + HST or $458 CAD for the battery, they
did not offer any refund for the old battery core and this did not include
any cost for installation.

I ended up purchasing a battery from Advance AutoParts in Niagara. They
had an exact replacement battery (Made in Germany) for $162 USD. I
ordered it online for pickup at the store. During checkout, they had a
promotion going on for $30 off purchases over $150, so in the end the
battery cost me $132+tax or $143.00 USD. And they gave me $5.00 back
for the old battery core and offered free installation if I wanted.

The battery fit perfectly, and has a 3 yr full replacement warranty and
is prorated after that.

AUTOCRAFT GOLD 95R/H9 950 CCA

Here is a shot of the battery sizes. I got this off the E39 list. My battery
is exactly the same, only has a 6/2011 date.

Ended up with an Exide Performance Group 49 battery, 10-7249-4. 850CCA, 160 RC. Pretty sure it's a traditional wet-cell (not AGM) battery, but has vents on both sides, so no extension required, you just need to plug the one on the -'ve side. Because it's a Group 49, it's slightly smaller than the 95R and just needed some spacers (rags, cloth, bubbles, etc.) to fit. Felt significantly lighter than the OEM mammoth (64lb) but didn't measure.